Wednesday 9 November 2011 02.51 EST
First published on Wednesday 9 November 2011 02.51 EST

The stinging resignation statement issued by Brodie Clark, the top civil servant in the border checks row, claims he felt unable to wait for internal inquiries into the controversy because Theresa May had already made his position untenable.

The home secretary's repeated claims that Clark was to blame for the reduction in passport checks at Britain's borders were wrong, and her decision to go to the Commons home affairs select committee on Tuesday – had made his position untenable, he said.

"Those statements were wrong and were made without the benefit of hearing my response to formal allegations," the statement, issued by the civil servants' union the FDA, said.

"With the home secretary announcing and repeating her view that I am at fault, I cannot see how any process conducted by the Home Office, or under its auspices, can be fair and balanced."

He said May had accused him of improperly taking "additional measures" beyond those agreed with ministers in July for a four-month trial of risk-based passport checks. "I did not," the statement said. "Those measures have been in place since 2008-2009."

Brodie said he had been pressing for the trial to go ahead since December 2010, and was pleased when May finally agreed to the pilot scheme.

"The evidence to support [such schemes] is substantial and the early findings are encouraging. I would do nothing to jeopardise them," he said. "I firmly believe that a more fully risk-based way of operating will offer far greater protection to the United Kingdom."

Jonathan Baume, the general secretary of the FDA, told the BBC: "He is very bruised, quite battered. This is a very gruelling experience for someone to be in the public glare.

"What he [Clark] is angry about is the fact that issues were raised – he was quite willing to answer those internally. But instead he was suspended and the home secretary has spent two days basically traducing him and damning him."

Clark's resignation enables him to appear before the Commons home affairs committee next Tuesday, and he said he had been advised to say nothing more until then.

Not waiting for the outcome of the three internal Home Office inquiries means his resignation decision is likely to cost him financially.

He had been suspended, along with two border force directors, pending the outcome of the inquiries.

The UK Border Agency's chief executive, Rob Whiteman, said: "Brodie Clark admitted to me on 2 November that, on a number of occasions this year, he authorised his staff to go further than ministerial instruction.

"I therefore suspended him from his duties. In my opinion, it was right for officials to have recommended the pilot so that we focus attention on higher risks to our border, but it is unacceptable that one of my senior officials went further than was approved."

The FDA said Clark had been treated with contempt by May. "It's astonishing that the home secretary [declared] him guilty before he had a chance of responding," the FDA national officer, Paul Whiteman, said.

A second civil service union, the PCS, said he had been "shamefully hung out to dry" by May, whose position "is now surely untenable".

The shadow home secretary, Yvette Cooper, said: "This fiasco gets worse for the home secretary. Now her version of events has been contradicted by her most senior official at the UK border force.

"First she decided to reduce border checks, then lost control of her so-called pilot. Now she has lost the loyalty of one of her most senior civil servants."

But May told MPs she would not go. She said the limited pilot scheme to which she had agreed was an operational matter that did not need cabinet approval and had not put border security at risk.

The intelligence-led checks had boosted interceptions of illegal migrants by 10%, she said. But Clark had gone further and relaxed border checks on travellers from outside Europe, for which he had to take full responsibility, she said.

David Cameron later backed May. He acknowledged that the limited pilot scheme had boosted arrest rates by 10% by having a lighter, targeted, passport control, but said there was clearly activity by the border force "that was not acceptable, and it is not acceptable that it went on for so long", he added, referring to the decision to extend the pilot in September.

A Labour motion to be debated in the Commons on Wednesday calls on the government to publish all instructions May gave to UKBA about passport checks this summer.

Labour is also questioning how a scheme that potentially applied to every port and airport in Britain and may have led to lighter passport checks on nearly two-thirds of passengers could be described as a pilot.Keith Vaz, the Labour chairman of the select committee, said Clark's statement had "cast very serious doubt" on the home secretary's account to his committee.

"It's completely contradictory to what she said," Vaz told the BBC. "This is a complete turnaround of events." Vaz's committee is to hear from Brodie next week.